title: K562PositiveSingle, rep35

tag: tissue

tag: cell line

tag: tpa time

tag: has mung_bean


title: K562PositiveSingle, rep38

status: Public on Oct 19 2023

type: SRA

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

country: USA

institute: University of Pennsylvania

library_source: genomic

data_processing:
Base calls and demultiplexed using bcl2fastq v2.17. Reads were first preprocessed by a customized SCAP-T Next Generation Sequencing pipeline (https://github.com/safisher/ngs), then mapped back to the Gencode GRCh38 (human) or UCSC mm10 (mouse) genome. Further, an additional QC procedure was applied to filter for high-quality reads with respect to the barcode/primer quality as well as the alignment quality. Basically, reads that qualify the A, B and C barcode/primer class are retained. Afterwards, reads that are less than 20bp (non-redundant length if paired) or have more than 10% mismatches are filtered out. Finally, reads that are mapped to low-quality genomic regions (defined by synthetic single-end 20bp reads that are mis-aligned to respective genomes) are removed. In addition, the ENCODE listed blacklist (https://sites.google.com/site/anshulkundaje/projects/blacklists) for human or mouse was used to mask the promiscuous regions. Finally, the starts (i.e. 5' end) of priming sites were called and output in the BED format, which were used for priming frequency estimation.
For priming start sites, we used R package ChIPseeker (v1.20.0) to annnote their genomic location with respect to promoter proximal as well as distal regions. To estimate the priming frequency, we used R package GenomicRanges v1.34.0. For priming frequency estimation, we used an in-house procedure to generate the aggreated coverage profiles at various genomic features, including TSS, gene body, intergenic, exon, intron, CDS. The genome annotation used for human was Ensembl v86 (via R package EnsDb.Hsapiens.v86), and for mouse was Ensembl v79 (via R package EnsDb.Mmusculus.v79).
Assembly: hg38, mm10
Supplementary files format and content: BED files containing the 5' location of CHEX-seq probe priming
Library strategy: CHEX-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: bone marrow

growth_protocol: K562 cells were obtained from ATCC and cultured in RPMI 1640 medium (Invitrogen) with 10% FBS and penicillin-streptomycin in a T75 flask at 37 °C in 5% CO2 for 2~3 days. HumanInterneuronCulture samples were derived from human induced pluripotent stem cells (iPSCs), where Stewart-4wk-human stem cells from the Children's Hospital of Philadelphia (CHOP) were plated on rat cortical neuronal feeders-1 and selected by interneuron promoter Lhx6-driven GFP expression. For mouse samples, a 3-month old male mouse was anaesthetized with halothane, euthanized by thoracotomy, then subjected to cardiac perfusion with 5 ml PBS followed by 20 ml PBS/4% paraformaldehyde. The brain was removed and post fixed at 4 °C for 16 hr., then rinsed in PBS and sectioned in the coronal plane at 100 μm on a vibratome (Leica VT-1000s). Sections including the hippocampus were then subjected to immunofluorescence labeling with chicken anti-MAP2 antisera (1:1000; Ab 5392; Abcam) followed by Alexa 488 conjugated goat anti-chicken secondary antibody (1:400; ab150169; Abcam).

extract_protocol:
After fixation and permeabilization, the cells and brain slices were incubated with CHEX-seq probe (170 nM) in TES buffer (10 mM Tris, 1 mM EDTA, 150 mM NaCl) for 1 hr at room temperature. The samples were then washed with 1x PBS (w/o Ca++, Mg++) 3 times for 3 min. After CHEX-seq probe annealing and washing, the samples were transferred to the imaging chamber with 1x PBS (w/o Ca++, Mg++). All images and photoactivations were performed using a Carl Zeiss 710 Meta confocal microscope (20x water-immersion objectives, NA 1.0). CHEX-seq probe annealing was confirmed by exciting at 633 nm and emission was detected at 640-747 nm. The photoactivation was performed using the 405 nm (UV) laser at 60% power and 6.30 μs per pixel. After photoactivation in each individual cell’s nucleus, a master mix containing DNA polymerase I and 1st strand DNA synthesis buffer was added to the cells and incubated for 1 h at room temperature. Subsequently, the single cells containing synthesized complementary DNA were harvested using a glass micropipette under using a Zeiss 710 confocal microscope (Carl Zeiss) for visualization.
(A) 1st strand DNA synthesis and poly G tailing at 3’ end: After harvesting single cells, the in situ synthesized cDNA was removed by adding fresh prepared 0.1 N NaOH and incubating the sample for 5 min at RT followed by neutralization with 1 M Tris (pH 7.5). After ethanol precipitation, the 1st strand DNA was resuspended in nuclease free water. Subsequently, poly(G) was added to the 3’ end using terminal deoxynucleotidyl transferase (TdT) (Invitrogen). (B) 2nd strand DNA synthesis and round 1 linear RNA amplification: 2nd strand DNA was synthesized using DNA polymerase I for 2 h at 16 °C after priming with custom App-RC-polyC primer (Supplemental Data, Table 1). RNA was amplified using linear in vitro transcription from T7 RNA polymerase promoter incorporated into the double-stranded DNA with Ambion MEGAscript T7 In Vitro Transcription (IVT) Kit. (C) Round 2 1st and 2nd strand DNA synthesis and PCR amplification: After cleanup IVT reaction, 1st strand DNA was reverse transcribed from aRNA using Superscript III using a custom App-RC primer (Supplemental Data, Table 1) 2nd strand DNA was synthesized using DNA Polymerase 1 with a custom 18bpPBC1 primer (Supplemental Data, Table 1). Subsequently, the double-stranded blunt ended DNA was amplified using custom primers 18bpPBC1 / App-RC (Supplemental Data, Table 1) following PCR condition: 98 °C for 30 sec; thermocycling at 98 °C for 10 sec, 50 °C for 30 sec, 72 °C for 30 sec for 27 cycles; extension at 72 °C for 2 mins, and was then used for library construction. Samples for the control experiments were processed with the same procedure except no CHEX-seq probe was applied, and 2nd round 2nd strand DNA PCR amplification was performed with custom primers 18bpPBC14 / App-RC. Illumina TruSeq Nano DNA Library Preparation Kit was used with modifications. All of the second round PCR amplified double-stranded DNA was used as input. After converting DNA fragment into blunt ends with End Repair Mix, base “A” was added; sequence adapters were ligated. DNA inserts were amplified with PCR.

treatment_protocol: The cultured cells were transferred to a 50 ml tube and 16% paraformaldehyde (final 1%) was added for 10 mins at room temperature to fix the cells. After fixation, 1 M glycine (final 200 mM) with RPMI 1640 medium was used to quench for 10 mins followed by centrifugation at 300 x g for 5 mins. The supernatant was discarded and - 3 mL of PBS were added to the pellet and then mixed by gently pipetting up and down 10-15 times using a fire-polished glass-pipette, to prevent cell clumping, and centrifuged at 300 rpm for 5 mins. The 100 μl cell pellet was attached to 18 mm gridded coverslips by incubating them for 2 hr. at room temperature. The samples were treated with PBS (w/o Ca++, Mg++) containing 0.01% Triton X-100 for 10 mins and then washed with PBS (w/o Ca++, Mg++) 3 times for 3 mins. To prepare human neuronal cell cultures, adult human brain tissue was placed in the papain (20 U, Worthington Biochemical) solution to dissociate at 37 °C for 30 to 40 mins and followed by ovomucoid (a papain inhibitor, 10 mg/ml, Worthington Biochemical) to stop the enzymatic dissociation. The tissue was triturated with a fire-polished glass Pasteur pipette. The cloudy cell suspension was carefully transferred to a new tube and centrifuged at 300 x g for 5 mins at room temperature. The cells were counted in an Autocounter (Invitrogen). Cells were plated on poly-L-lysine-coated (0.1 mg/ml, Sigma-Aldrich) 12-mm coverslips at a density of 3 × 104 cells/coverslip. Cultures were incubated at 37 °C, 95% humidity, and 5% CO2 in neuronal basal medium (Neurobasal A, Gibco), serum-free supplement (B-27, Gibco) and 1% penicillin/streptomycin (Thermo-Fisher Scientific). Dispersed mouse neuron/astrocyte cultures were prepared following published protocols. Dispersed cells were fixed using 4% paraformaldehyde for 10 min at room temperature. This was followed by three washes with 1x PBS. The cells were permeabolized with 0.1% Triton-X100 for 10 min at room temperature followed by three washes with 1x PBS.

value: bone marrow

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value: culture

tag: has tpa

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tag: is negative_control

tag: composition

value: Single

tag: biological group

tag: treatment group

value: PositiveSingle


title: K562PositiveSingle, rep56

tag: tissue

tag: cell line

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tag: has mung_bean


title: K562PositiveSingle, rep32

tag: cell type

tag: genotype

tag: probe id

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title: K562PositiveSingle, rep34

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tag: has probe

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title: K562PositiveSingle, rep52

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title: K562PositiveSingle, rep36

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title: K562PositiveSingle, rep54

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title: K562PositiveSingle, rep33

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title: K562PositiveSingle, rep31

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title: K562PositiveSingle, rep50

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title: K562PositiveSingle, rep30

tag: is negative_control

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title: K562PositiveSingle, rep27

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title: K562PositiveSingle, rep29

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title: K562PositiveSingle, rep24

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title: K562PositiveSingle, rep23

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title: K562PositiveSingle, rep20

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title: K562PositiveSingle, rep21

tag: tissue

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title: K562PositiveSingle, rep18

tag: cell type

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title: K562PositiveSingle, rep28

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title: K562PositiveSingle, rep43

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title: K562PositiveSingle, rep14

tag: is negative_control

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title: K562PositiveSingle, rep26

tag: tissue

tag: cell line

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title: K562PositiveSingle, rep25

tag: cell type

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tag: probe id

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title: K562PositiveSingle, rep11

tag: primer pc

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title: K562PositiveSingle, rep10

tag: cell count

tag: harvest method

tag: has tpa

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title: K562PositiveSingle, rep12

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title: K562PositiveSingle, rep22

tag: tissue

tag: cell line

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title: K562PositiveSingle, rep19

tag: cell type

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title: K562PositiveSingle, rep13

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title: K562PositiveSingle, rep2

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title: K562PositiveSingle, rep16

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title: K562PositiveSingle, rep15

tag: tissue

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title: K562PositiveBulk, rep4

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value: Bulk

value: PositiveBulk


title: K562PositiveSingle, rep6

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title: K562PositiveBulk, rep2

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title: K562PositiveSingle, rep9

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title: K562PositiveSingle, rep1

tag: tissue

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title: K562PositiveSingle, rep8

tag: cell type

tag: genotype

tag: probe id

tag: primer 2p


title: K562NegCtrlSingle, rep15

tag: primer pc

tag: has probe

tag: has laser405

tag: has laser633

value: NegCtrlSingle


title: K562NegCtrlSingle, rep13

tag: cell count

tag: harvest method

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tag: tpa dose


title: K562PositiveSingle, rep7

tag: is negative_control

tag: composition

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title: K562NegCtrlSingle, rep10

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title: K562PositiveSingle, rep3

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tag: probe id

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title: K562PositiveSingle, rep4

tag: primer pc

tag: has probe

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title: K562PositiveBulk, rep6

tag: cell count

tag: harvest method

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tag: tpa dose


title: K562PositiveSingle, rep5

tag: is negative_control

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tag: biological group

tag: treatment group


title: K562NegCtrlSingle, rep9

tag: tissue

tag: cell line

tag: tpa time

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title: K562NegCtrlSingle, rep7

tag: cell type

tag: genotype

tag: probe id

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title: K562PositiveBulk, rep5

tag: primer pc

tag: has probe

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title: K562NegCtrlSingle, rep8

tag: cell count

tag: harvest method

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tag: tpa dose


title: K562NegCtrlSingle, rep17

tag: is negative_control

tag: composition

tag: biological group

tag: treatment group


title: K562NegCtrlSingle, rep16

tag: tissue

tag: cell line

tag: tpa time

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title: K562PositiveSingle, rep17

tag: cell type

tag: genotype

tag: probe id

tag: primer 2p


title: K562PositiveBulk, rep3

tag: primer pc

tag: has probe

tag: has laser405

tag: has laser633


title: K562NegCtrlSingle, rep1

tag: cell count

tag: harvest method

tag: has tpa

tag: tpa dose


title: K562PositiveBulk, rep1

tag: is negative_control

tag: composition

tag: biological group

tag: treatment group


title: K562NegCtrlSingle, rep2

tag: tissue

tag: cell line

tag: tpa time

tag: has mung_bean


title: K562NegCtrlBulk, rep2

tag: cell type

tag: genotype

tag: probe id

tag: primer 2p

value: NegCtrlBulk


title: K562MungBeanPositiveSingle, rep13

tag: primer pc

tag: has probe

tag: has laser405

tag: has laser633


title: K562NegCtrlSingle, rep14

tag: cell count

tag: harvest method

tag: has tpa

tag: tpa dose


title: K562NegCtrlSingle, rep12

tag: is negative_control

tag: composition

tag: biological group

tag: treatment group


title: K562NegCtrlSingle, rep11

tag: tissue

tag: cell line

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title: K562MungBeanPositiveSingle, rep10

tag: cell type

tag: genotype

tag: probe id

tag: primer 2p


title: K562MungBeanPositiveSingle, rep11

tag: primer pc

tag: has probe

tag: has laser405

tag: has laser633


title: K562MungBeanPositiveSingle, rep9

tag: cell count

tag: harvest method

tag: has tpa

tag: tpa dose


title: K562MungBeanPositiveSingle, rep7

tag: is negative_control

tag: composition

tag: biological group

tag: treatment group


title: K562MungBeanPositiveSingle, rep8

tag: tissue

tag: cell line

tag: tpa time

tag: has mung_bean


title: K562NegCtrlSingle, rep5

tag: cell type

tag: genotype

tag: probe id

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title: K562MungBeanPositiveSingle, rep6

tag: primer pc

tag: has probe

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title: K562NegCtrlSingle, rep3

tag: cell count

tag: harvest method

tag: has tpa

tag: tpa dose


title: K562NegCtrlSingle, rep4

tag: is negative_control

tag: composition

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title: K562NegCtrlSingle, rep6

tag: tissue

tag: cell line

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title: K562MungBeanPositiveSingle, rep2

tag: cell type

tag: genotype

tag: probe id

tag: primer 2p


title: K562MungBeanPositiveSingle, rep14

tag: primer pc

tag: has probe

tag: has laser405

tag: has laser633


title: HumanInterneuronCulturePositiveSingle, rep20

description: HumanInterneuronCulturePositiveSingle

source_name: stem cell

value: stem cell

value: interneuron

tag: cell count

tag: harvest method

tag: has tpa

tag: tpa dose

value: HumanInterneuronCulture


title: K562NegCtrlBulk, rep1

tag: is negative_control

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description: HumanInterneuronCulturePositiveSingle

tag: tissue

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title: HumanInterneuronCulturePositiveSingle, rep19

description: HumanInterneuronCulturePositiveSingle

tag: cell type

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tag: probe id

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description: HumanInterneuronCulturePositiveSingle

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description: HumanInterneuronCulturePositiveSingle

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tag: tpa dose


title: HumanInterneuronCulturePositiveSingle, rep15

description: HumanInterneuronCulturePositiveSingle

tag: is negative_control

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tag: treatment group


title: HumanInterneuronCulturePositiveSingle, rep10

description: HumanInterneuronCulturePositiveSingle

tag: tissue

tag: cell line

tag: tpa time

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title: HumanInterneuronCulturePositiveSingle, rep8

description: HumanInterneuronCulturePositiveSingle

tag: cell type

tag: genotype

tag: probe id

tag: primer 2p


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description: HumanInterneuronCulturePositiveSingle

tag: primer pc

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description: HumanInterneuronCulturePositiveSingle

tag: cell count

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tag: tpa dose


title: K562MungBeanPositiveSingle, rep12

tag: is negative_control

tag: composition

tag: biological group

tag: treatment group


title: K562MungBeanPositiveSingle, rep5

tag: tissue

tag: cell line

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title: HumanInterneuronCulturePositiveSingle, rep13

description: HumanInterneuronCulturePositiveSingle

tag: cell type

tag: genotype

tag: probe id

tag: primer 2p


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description: HumanInterneuronCulturePositiveSingle

tag: primer pc

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tag: has laser633


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tag: cell count

tag: harvest method

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tag: tpa dose


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tag: is negative_control

tag: composition

tag: biological group

tag: treatment group


title: K562MungBeanPositiveSingle, rep1

tag: tissue

tag: cell line

tag: tpa time

tag: has mung_bean


title: HumanInterneuronCulturePositiveSingle, rep1

description: HumanInterneuronCulturePositiveSingle

tag: cell type

tag: genotype

tag: probe id

tag: primer 2p


title: HumanInterneuronCulturePositiveSingle, rep5

description: HumanInterneuronCulturePositiveSingle

tag: primer pc

tag: has probe

tag: has laser405

tag: has laser633


title: mouse interneuron, rep8

description:
mouse interneuron
MouseBrainRNAExonCnts.csv.gz
MouseBrainRNAIntronCnts.csv.gz

library_source: transcriptomic

data_processing:
Base calls and demultiplexed using bcl2fastq v2.17. Reads were preprocessed by SCAP-T Next Generation Sequencing pipeline (https://github.com/safisher/ngs) using STAR v2.4.0 (Dobin et al. 2013).
Uniquely mapped reads were used for gene quantification using VERSE v0.1.4 with parameters "-s 1 -z 3 --nonemptyModified" (Zhu et al. 2016, doi:https://doi.org/10.1101/053306).
Assembly: mm10
Supplementary files format and content: csv files containing mouse brain single-cell raw exonic or intronic counts

molecule: total RNA

organism: Mus musculus

source_name: cortex

growth_protocol: For cultured astrocytes and neurons, a 3-month old male mouse was anaesthetized with halothane, euthanized by thoracotomy, then subjected to cardiac perfusion with 5 ml PBS followed by 20 ml PBS/4% paraformaldehyde. For sliced interneurons, we used standard brain slice preparation technology (see GSE135060).

extract_protocol:
For cultured astrocytes and neurons, the brain was removed and post fixed at 4 °C for 16 hr., then rinsed in PBS and sectioned in the coronal plane at 100 μm on a vibratome (Leica VT-1000s). Sections including the hippocampus were then subjected to immunofluorescence labeling with chicken anti-MAP2 antisera (1:1000;Ab 5392; Abcam) followed by Alexa 488 conjugated goat anti-chicken secondary antibody (1:400;ab150169; Abcam). For sliced interneurons, mice were quickly anesthetized in 2% isoflurane, and decapitated. Brains were removed and laced into ice cold artificial cerebrospinal fluid (ACSF). Slices were cut by vibratome (Leica VT1000 S, Leica Biosystems, Wetzlar, Germany) under ice cold ACSF supplied with Carbogen (5% CO2 in 95% oxygen), then were stored in storage ACSF on room temperature in a chamber and permanently supplied by Carbogen for 1 hour before recording. Three hundred µm slices were cut from a mouse brain so that we were able to collect cells from different layers from the prefrontal cortex (PFC). Individual cells were collected by patch-clamp pipette.
For cultured astrocytes and neurons,Illumina TruSeq Nano DNA Library Preparation Kit was used with modifications. All of the second round PCR amplified double-stranded DNA was used as input. After converting DNA fragment into blunt ends with End Repair Mix, base “A” was added; sequence adapters were ligated. DNA inserts were amplified with PCR and sequenced by NextSeq 500. For sliced interneurons, libraries were made with Illumina TruSeq Stranded kit (RS-122-2101/2) and sequenced by Illumina HiSeq 2500.

value: cortex

tag: condition

value: acute slice

tag: harvest method

value: patch clamp pipette


title: HumanInterneuronCulturePositiveSingle, rep9

description: HumanInterneuronCulturePositiveSingle

tag: cell count

tag: has tpa

tag: tpa dose

tag: is negative_control

tag: composition


title: HumanInterneuronCulturePositiveSingle, rep7

description: HumanInterneuronCulturePositiveSingle

tag: tissue

tag: cell line

tag: tpa time

tag: biological group

tag: treatment group


title: mouse interneuron, rep3

tag: genotype

tag: cell type


title: mouse neuron, rep12

description:
mouse neuron
MouseBrainRNAExonCnts.csv.gz
MouseBrainRNAIntronCnts.csv.gz

value: primary culture

value: neuron

value: pipette


title: mouse interneuron, rep1


title: mouse neuron, rep11


title: mouse interneuron, rep2


title: HumanInterneuronCulturePositiveSingle, rep3

description: HumanInterneuronCulturePositiveSingle

tag: probe id

tag: primer 2p

tag: primer pc

tag: has probe

value: Y

value: culture

tag: has mung_bean


title: HumanInterneuronCulturePositiveSingle, rep4

description: HumanInterneuronCulturePositiveSingle

tag: has laser405

tag: has laser633

tag: cell count

tag: harvest method

value: N

value: Single


title: HumanInterneuronCulturePositiveSingle, rep2

description: HumanInterneuronCulturePositiveSingle

tag: has tpa

tag: tpa dose

tag: is negative_control

tag: composition

value: PositiveSingle


title: mouse interneuron, rep7

tag: tissue

tag: condition


title: mouse interneuron, rep6

tag: genotype


title: mouse neuron, rep9

tag: cell type


title: HumanInterneuronCulturePositiveSingle, rep14

description: HumanInterneuronCulturePositiveSingle

tag: cell line

tag: probe id

tag: tpa time

tag: biological group

tag: treatment group


title: mouse interneuron, rep4


title: mouse interneuron, rep5


title: mouse neuron, rep4


title: mouse neuron, rep5


title: mouse neuron, rep10


title: mouse neuron, rep8


title: mouse neuron, rep7


title: mouse neuron, rep1


title: mouse astrocyte, rep4

description:
mouse astrocyte
MouseBrainRNAExonCnts.csv.gz
MouseBrainRNAIntronCnts.csv.gz

value: astrocyte


title: mouse neuron, rep6


title: mouse astrocyte, rep7


title: mouse astrocyte, rep8


title: mouse neuron, rep3


title: mouse astrocyte, rep5


title: mouse astrocyte, rep3


title: mouse neuron, rep2


title: MouseNeuronSlicePositiveSingle, rep26

description: MouseNeuronSlicePositiveSingle

source_name: brain

value: brain

tag: primer 2p

tag: primer pc

tag: has probe

tag: has laser405

value: tissue section

tag: has mung_bean

value: MouseNeuronSlice


title: mouse astrocyte, rep6

tag: harvest method


title: mouse astrocyte, rep2


title: MouseNeuronSlicePositiveSingle, rep22

description: MouseNeuronSlicePositiveSingle

tag: has laser633

tag: cell count

tag: has tpa

tag: tpa dose

tag: is negative_control


title: MouseNeuronSlicePositiveSingle, rep25

description: MouseNeuronSlicePositiveSingle

tag: tissue

tag: cell type

tag: genotype

tag: composition


title: MouseNeuronSlicePositiveSingle, rep18

description: MouseNeuronSlicePositiveSingle

tag: cell line

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description: MouseNeuronSlicePositiveSingle

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description: MouseNeuronSlicePositiveSingle

tag: has laser405

tag: has laser633

tag: harvest method

tag: has mung_bean


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description: MouseNeuronSlicePositiveSingle

tag: cell count

tag: has tpa

tag: tpa dose

tag: is negative_control


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description: MouseNeuronSlicePositiveSingle

tag: tissue

tag: cell type

tag: genotype

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title: MouseNeuronSlicePositiveSingle, rep23

description: MouseNeuronSlicePositiveSingle

tag: cell line

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description: MouseNeuronSlicePositiveSingle

tag: primer 2p

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description: MouseNeuronSlicePositiveSingle

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description: MouseNeuronSlicePositiveSingle

tag: cell count

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tag: is negative_control


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description: MouseNeuronSlicePositiveSingle

tag: tissue

tag: cell type

tag: genotype

tag: composition


title: MouseNeuronSlicePositiveSingle, rep15

description: MouseNeuronSlicePositiveSingle

tag: cell line

tag: probe id

tag: tpa time

tag: biological group


title: MouseNeuronSlicePositiveSingle, rep9

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title: MouseNeuronSlicePositiveSingle, rep11

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title: MouseNeuronCulturePositiveSingle, rep127

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title: MouseNeuronCulturePositiveSingle, rep122

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title: MouseNeuronCulturePositiveSingle, rep115

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title: MouseNeuronCulturePositiveSingle, rep107

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title: MouseNeuronCulturePositiveSingle, rep126

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title: MouseNeuronCulturePositiveSingle, rep100

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title: MouseNeuronCulturePositiveSingle, rep99

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title: MouseNeuronCulturePositiveSingle, rep97

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title: MouseNeuronCulturePositiveSingle, rep98

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title: MouseNeuronCulturePositiveSingle, rep95

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title: MouseNeuronCulturePositiveSingle, rep92

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title: MouseNeuronCulturePositiveSingle, rep36

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title: MouseNeuronCulturePositiveSingle, rep28

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title: MouseNeuronCulturePositiveSingle, rep34

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title: MouseNeuronCulturePositiveSingle, rep26

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title: MouseNeuronCulturePositiveSingle, rep18

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title: MouseNeuronCulturePositiveSingle, rep15

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title: MouseNeuronCulturePositiveSingle, rep20

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title: MouseNeuronCultureNegCtrlSingle, rep4

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title: MouseNeuronCulturePositiveSingle, rep4

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title: MouseInterneuronSlicePositiveSingle, rep14

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title: MouseInterneuronSlicePositiveSingle, rep10

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title: MouseNeuronCultureNegCtrlSingle, rep3

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title: MouseInterneuronSlicePositiveSingle, rep8

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tag: primer 2p

tag: primer pc

tag: has probe

tag: treatment group


title: MouseNeuronCultureNegCtrlSingle, rep1

description: MouseNeuronCultureNegCtrlSingle

tag: has laser405

tag: has laser633

tag: cell count

tag: harvest method


title: MouseInterneuronSlicePositiveSingle, rep7

description: MouseInterneuronSlicePositiveSingle

tag: tissue

tag: cell type

tag: has tpa

tag: has mung_bean


title: MouseInterneuronSlicePositiveSingle, rep5

description: MouseInterneuronSlicePositiveSingle

tag: cell line

tag: genotype

tag: tpa dose

tag: is negative_control


title: MouseInterneuronSlicePositiveSingle, rep18

description: MouseInterneuronSlicePositiveSingle

tag: probe id

tag: tpa time

tag: composition

tag: biological group


title: MouseInterneuronSlicePositiveSingle, rep20

description: MouseInterneuronSlicePositiveSingle

tag: primer 2p

tag: primer pc

tag: has probe

tag: treatment group


title: MouseInterneuronSlicePositiveSingle, rep2

description: MouseInterneuronSlicePositiveSingle

tag: has laser405

tag: has laser633

tag: cell count

tag: harvest method


title: MouseInterneuronSlicePositiveSingle, rep3

description: MouseInterneuronSlicePositiveSingle

tag: tissue

tag: cell type

tag: has tpa

tag: has mung_bean


title: MouseAstroCulturePositiveSingle, rep34

description: MouseAstroCulturePositiveSingle

tag: cell line

value: astrocyte

tag: genotype

tag: tpa dose

tag: is negative_control

value: MouseAstroCulture


title: MouseInterneuronSlicePositiveSingle, rep1

description: MouseInterneuronSlicePositiveSingle

value: brain

tag: probe id

value: tissue section

tag: tpa time

tag: composition

tag: biological group


title: MouseAstroCulturePositiveSingle, rep31

description: MouseAstroCulturePositiveSingle

tag: primer 2p

tag: primer pc

tag: has probe

tag: treatment group


title: MouseAstroCulturePositiveSingle, rep35

description: MouseAstroCulturePositiveSingle

tag: has laser405

tag: has laser633

tag: cell count

tag: harvest method


title: MouseAstroCulturePositiveSingle, rep30

description: MouseAstroCulturePositiveSingle

tag: tissue

tag: cell type

tag: has tpa

tag: has mung_bean


title: MouseAstroCulturePositiveSingle, rep33

description: MouseAstroCulturePositiveSingle

tag: cell line

tag: genotype

tag: tpa dose

tag: is negative_control


title: MouseAstroCulturePositiveSingle, rep27

description: MouseAstroCulturePositiveSingle

tag: probe id

tag: tpa time

tag: composition

tag: biological group


title: MouseAstroCulturePositiveSingle, rep28

description: MouseAstroCulturePositiveSingle

tag: primer 2p

tag: primer pc

tag: has probe

tag: treatment group


title: MouseAstroCulturePositiveSingle, rep32

description: MouseAstroCulturePositiveSingle

tag: has laser405

tag: has laser633

tag: cell count

tag: harvest method


title: MouseAstroCulturePositiveSingle, rep29

description: MouseAstroCulturePositiveSingle

tag: tissue

tag: cell type

tag: has tpa

tag: has mung_bean


title: MouseAstroCulturePositiveSingle, rep23

description: MouseAstroCulturePositiveSingle

tag: cell line

tag: genotype

tag: tpa dose

tag: is negative_control


title: MouseAstroCulturePositiveSingle, rep24

description: MouseAstroCulturePositiveSingle

tag: probe id

tag: tpa time

tag: composition

tag: biological group


title: MouseAstroCulturePositiveSingle, rep22

description: MouseAstroCulturePositiveSingle

tag: primer 2p

tag: primer pc

tag: has probe

tag: treatment group


title: MouseAstroCulturePositiveSingle, rep25

description: MouseAstroCulturePositiveSingle

tag: has laser405

tag: has laser633

tag: cell count

tag: harvest method


title: MouseAstroCulturePositiveSingle, rep21

description: MouseAstroCulturePositiveSingle

tag: tissue

tag: cell type

tag: has tpa

tag: has mung_bean


title: MouseInterneuronSlicePositiveSingle, rep6

description: MouseInterneuronSlicePositiveSingle

tag: cell line

tag: genotype

tag: tpa dose

tag: is negative_control


title: MouseAstroCulturePositiveSingle, rep20

description: MouseAstroCulturePositiveSingle

tag: probe id

tag: tpa time

tag: composition

tag: biological group


title: MouseAstroCulturePositiveSingle, rep17

description: MouseAstroCulturePositiveSingle

tag: primer 2p

tag: primer pc

tag: has probe

tag: treatment group


title: MouseAstroCulturePositiveSingle, rep19

description: MouseAstroCulturePositiveSingle

tag: has laser405

tag: has laser633

tag: cell count

tag: harvest method


title: MouseAstroCulturePositiveSingle, rep16

description: MouseAstroCulturePositiveSingle

tag: tissue

tag: cell type

tag: has tpa

tag: has mung_bean


title: MouseAstroCulturePositiveSingle, rep18

description: MouseAstroCulturePositiveSingle

tag: cell line

tag: genotype

tag: tpa dose

tag: is negative_control


title: MouseInterneuronSlicePositiveSingle, rep4

description: MouseInterneuronSlicePositiveSingle

tag: probe id

tag: tpa time

tag: composition

tag: biological group


title: MouseAstroCulturePositiveSingle, rep15

description: MouseAstroCulturePositiveSingle

tag: primer 2p

tag: primer pc

tag: has probe

tag: treatment group


title: MouseAstroCulturePositiveSingle, rep26

description: MouseAstroCulturePositiveSingle

tag: has laser405

tag: has laser633

tag: cell count

tag: harvest method


title: MouseAstroCulturePositiveSingle, rep13

description: MouseAstroCulturePositiveSingle

tag: tissue

tag: cell type

tag: has tpa

tag: has mung_bean


title: MouseAstroCulturePositiveSingle, rep14

description: MouseAstroCulturePositiveSingle

tag: cell line

tag: genotype

tag: tpa dose

tag: is negative_control


title: MouseAstroCulturePositiveSingle, rep11

description: MouseAstroCulturePositiveSingle

tag: probe id

tag: tpa time

tag: composition

tag: biological group


title: MouseAstroCulturePositiveSingle, rep12

description: MouseAstroCulturePositiveSingle

tag: primer 2p

tag: primer pc

tag: has probe

tag: treatment group


title: MouseAstroCulturePositiveSingle, rep10

description: MouseAstroCulturePositiveSingle

tag: has laser405

tag: has laser633

tag: cell count

tag: harvest method


title: MouseAstroCulturePositiveSingle, rep8

description: MouseAstroCulturePositiveSingle

tag: tissue

tag: cell type

tag: has tpa

tag: has mung_bean


title: MouseAstroCulturePositiveSingle, rep7

description: MouseAstroCulturePositiveSingle

tag: cell line

tag: genotype

tag: tpa dose

tag: is negative_control


title: MouseAstroCulturePositiveSingle, rep1

description: MouseAstroCulturePositiveSingle

tag: probe id

tag: tpa time

tag: composition

tag: biological group


title: MouseAstroCulturePositiveSingle, rep5

description: MouseAstroCulturePositiveSingle

tag: primer 2p

tag: primer pc

tag: has probe

tag: treatment group


title: MouseAstroCulturePositiveBulk, rep3

description: MouseAstroCulturePositiveBulk

tag: has laser405

tag: has laser633

tag: cell count

tag: harvest method

value: Bulk


title: MouseAstroCulturePositiveSingle, rep2

description: MouseAstroCulturePositiveSingle

tag: tissue

tag: cell type

tag: has tpa

tag: has mung_bean


title: MouseAstroCulturePositiveBulk, rep2

description: MouseAstroCulturePositiveBulk

tag: cell line

tag: genotype

tag: tpa dose

tag: is negative_control


title: MouseAstroCulturePositiveBulk, rep1

description: MouseAstroCulturePositiveBulk

tag: probe id

tag: tpa time

tag: composition

tag: biological group


title: MouseAstroCultureNegCtrlSingle, rep5

description: MouseAstroCultureNegCtrlSingle

tag: primer 2p

tag: primer pc

tag: has probe

tag: treatment group


title: MouseAstroCultureNegCtrlSingle, rep4

description: MouseAstroCultureNegCtrlSingle

tag: has laser405

tag: has laser633

tag: cell count

tag: harvest method


title: MouseAstroCultureNegCtrlSingle, rep3

description: MouseAstroCultureNegCtrlSingle

tag: tissue

tag: cell type

tag: has tpa

tag: has mung_bean


title: MouseAstroCultureNegCtrlSingle, rep1

description: MouseAstroCultureNegCtrlSingle

tag: cell line

tag: genotype

tag: tpa dose

tag: is negative_control


title: MouseAstroCultureNegCtrlBulk, rep1

description: MouseAstroCultureNegCtrlBulk

tag: probe id

tag: tpa time

tag: composition

tag: biological group

value: NegCtrlBulk


title: MouseAstroCultureNegCtrlSingle, rep2

description: MouseAstroCultureNegCtrlSingle

tag: primer 2p

tag: primer pc

tag: has probe

tag: treatment group


title: H1[ADAR] replicate 1

status: Public on Oct 10 2023

city: Haining

first: Huanchang

last: Tu

address: 718 East Haizhou Rd., Haining, Zhejiang

country: China

institute: Zhejiang University

data_processing:
The original fluorescence image files obtained from Illumina platform are transformed to short reads (Raw data) by base calling and these short reads are recorded in FASTQformat, which contains sequence information and corresponding sequencing quality information.
The raw data was accessed with FastQC (v0.11.9) for overall quality of the bulk RNA-seq fastq files, identifying any potential issues.
Paired-end sequencing was performed on the Bulk RNA-seq libraries, and the resulting reads were trimmed using cutadapt (v4.1).
Trimmed reads were mapped to the hg38 assembly with bowtie2 (v2.4.5), sorted with samtools (v1.6) and quantified against Gencode (v41) annotations using featureCounts (v2.0.1).
Assembly: hg38
Supplementary files format and content: txt files: counts of the samples
Supplementary files format and content: csv file: the matrix of counts for samples

molecule: polyA RNA

source_name: hESC

extract_protocol:
Total RNA was extracted from hESCs with the Trizol reagent (Thermo, 15596026) according to the manufacturer's instructions.
Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEB Next Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beverly, USA). Then 3 μL USER Enzyme (NEB, USA) was used with size selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent 5400 system(Agilent，USA) and quantified by QPCR (1.5 nM). The qualified libraries were pooled and sequenced on Illumina platforms with PE150 strategy in Novogene Bioinformatics Technology Co., Ltd (Beijing, China), according to effective library concentration and data amount required.

value: hESC

value: human embryonic stem cells

value: tetON-ADAR

tag: treatment

value: With doxycyclin for 24 hours


title: H1[ADAR] replicate 2


title: H1[hAPOBEC1] replicate 1

value: tetON-hAPOBEC


title: IGF2BP3-rAPOBEC1, replicate 2


title: H1[hAPOBEC1] replicate 2


title: MouseAstroCulturePositiveSingle, rep9

description: MouseAstroCulturePositiveSingle

tag: tissue

tag: has laser405

tag: has laser633

tag: cell count

tag: harvest method


title: IGF2BP3-rAPOBEC1, replicate 1

tag: cell line

tag: cell type

tag: genotype


title: IGF2BP3-hAPOBEC1, replicate 2


title: MouseAstroCulturePositiveSingle, rep4

description: MouseAstroCulturePositiveSingle

tag: probe id

tag: has tpa

tag: tpa dose

tag: has mung_bean

tag: is negative_control


title: IGF2BP3-ADAR, replicate 2


title: IGF2BP3-ADAR, replicate 1


title: IGF2BP3-hAPOBEC1, replicate 1


title: IGF2BP2-rAPOBEC1, replicate 2


title: IGF2BP2-rAPOBEC1, replicate 1


title: MouseAstroCulturePositiveSingle, rep6

description: MouseAstroCulturePositiveSingle

tag: primer 2p

tag: primer pc

tag: tpa time

tag: composition

tag: biological group


title: MouseAstroCulturePositiveSingle, rep3

description: MouseAstroCulturePositiveSingle

tag: tissue

tag: has probe

tag: has laser405

tag: treatment group


title: IGF2BP2-hAPOBEC1, replicate 1

tag: cell line

tag: treatment


title: IGF2BP2-ADAR, replicate 1

tag: cell type

tag: genotype


title: IGF2BP2-hAPOBEC1, replicate 2


title: IGF2BP1-rAPOBEC1, replicate 2


title: IGF2BP1-hAPOBEC1, replicate 2


title: IGF2BP2-ADAR, replicate 2


title: IGF2BP1-hAPOBEC1, replicate 1


title: WT_hESC, replicate 2

value: control


title: IGF2BP1-ADAR, replicate 1


title: WT_hESC, replicate 1


title: Sample_11-8-GC

status: Public on Oct 03 2023

city: Ås

first: Gabriela

last: Carril

address: Oluf Thesens vei 30

country: Norway

institute: Norwegian University of Life Sciences

description: 150 bp paired-end

data_processing:
Raw reads from RNA sequencing were trimmed using BBDuk (v34.56)
HISAT (v2.1.0) was used for genome alignment
The fragments mapped were counted with featureCounts (v1.4.6-1)
Differentially expressed genes (DEGs) between groups were estimated using SARTools (v1.7.3)
Assembly: Genome Psal-013 LF-89 (ASM970875v1 - RefSeq assembly accession: GCF_009708755.1)
Assembly: Genome Psal-182 EM-90 (ASM970941v1 - RefSeq assembly accession: GCF_009709415.1)
Supplementary files format and content: count files/txt files

organism: Piscirickettsia salmonis

growth_protocol: FN2 broth medium for culture bacteria until reach OD600nm of 0.2, then nine semi-permeable implants were inserted into the abdominal cavity of Atlantic salmon for 6 days

extract_protocol:
Total RNA was extracted from all the samples using Qiagen RNeasy Mini Kit (Qiagen) and QIAseq FastSelect −5S/16S/23S (Qiagen) was used for rRNA depletion
Library preparation and RNA-seq were performed at the Norwegian Sequencing Center (UiO, Norway)
TruSeq Stranded mRNA library prep

tag: strain

tag: culture

value: co-culture

tag: host

value: Salmo salar

tag: time

value: Day 6


title: Sample_12-9-GC

description: 150 bp paired-end


title: Sample_10-7-GC

description: 150 bp paired-end


title: mCRPC_18-030P4_RETROPERITONEAL

status: Public on Sep 19 2023

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

data_processing:
Sequencing reads were mapped to the hg38 human genome and mm10 mouse genomes using STAR.v2.7.3a. Sequences aligning to the mouse genome deriving from potential contamination with mouse tissue were removed from the analysis using XenofilteR (v1.6).
Gene level abundance was quantitated using the GenomicAlignments summarizeOverlaps function using mode=IntersectionStrict, restricting to primary aligned reads, and counting reads mapping to the exonic regions of genes.
Assembly: hg38
Supplementary files format and content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: CRPC retroperitoneal metastasis

extract_protocol:
Total RNA was isolated using RNA STAT-60 (Tel-Test). The isolated RNA was then purified with Qiagen RNeasy Kit (Qiagen Inc.) according to the manufacturer’s protocol utilizing the manufacturer’s recommended DNase digestion (Qiagen).
RNA-seq libraries were constructed from total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.

tag: Sex

value: male

value: CRPC metastasis

value: prostate cancer


title: mCRPC_18-030H4_LIVER

source_name: CRPC liver metastasis


title: mCRPC_18-030N3_LN

source_name: CRPC lymph node (LN) metastasis


title: mCRPC_17-113Q1_LUNG_PLEURAL

source_name: CRPC lung pleural metastasis


title: mCRPC_18-011I3_LIVER


title: mCRPC_17-108K4_LIVER


title: mCRPC_17-085O1_PERICABLE_LN

source_name: CRPC pericable lymph node (LN) metastasis


title: mCRPC_17-108H2_CHEST_WALL_MASS

source_name: CRPC chest wall mass metastasis


title: IGF2BP1-rAPOBEC1, replicate 1


title: mCRPC_17-081L7_LUNG

source_name: CRPC lung metastasis


title: mCRPC_17-081K3_LN


title: mCRPC_17-085I8_ABDOMINAL_FAT

source_name: CRPC abdominal fat metastasis


title: IGF2BP1-ADAR, replicate 2


title: mCRPC_17-081P8_PERIESOPHAGEAL

source_name: CRPC periesophageal metastasis


title: mCRPC_17-072K1_PERIHEPATIC

source_name: CRPC perihepatic metastasis


title: mCRPC_17-036N6_LN


title: mCRPC_17-033J1_PANCREAS

source_name: CRPC pancreas metastasis


title: mCRPC_17-022K1_LIVER


title: mCRPC_17-036H10_LIVER


title: mCRPC_17-017O4_LN


title: mCRPC_17-033H7_TAIL_OF_PANCREAS

source_name: CRPC tail of pancreas metastasis


title: mCRPC_17-072I2_SPLEEN

source_name: CRPC spleen metastasis


title: mCRPC_17-057J2_LIVER


title: mCRPC_17-036L3_LN


title: mCRPC_17-017K1_LIVER


title: mCRPC_17-017N1_LUNG


title: mCRPC_17-007H1_LIVER


title: mCRPC_17-001I2_PELVIC_MASS

source_name: CRPC pelvic mass metastasis


title: mCRPC_17-085J6_ABD_WALL_PERITONEUM

source_name: CRPC abdominal wall peritoneum metastasis


title: mCRPC_16-101J6_OMENTUM

source_name: CRPC omentum metastasis


title: mCRPC_17-017H8_LIVER


title: mCRPC_20-014H1_NE

source_name: CRPC liver metastasis (NE focus)


title: mCRPC_16-101N2_PARIETAL_DIAPHRAGM

source_name: CRPC parietal diaphragm metastasis


title: mCRPC_20-013_SKIN_MET2

source_name: CRPC skin metastasis


title: mCRPC_20-008J1_PERIAORTIC_LN

source_name: CRPC periaortic lymph node (LN) metastasis


title: mCRPC_20-014H1_ADC

source_name: CRPC liver metastasis (ADC focus)


title: mCRPC_19-074I1_BLADDER

source_name: CRPC bladder metastasis


title: mCRPC_16-080L2_LIVER

source_name: CRPC liver metastasis


title: mCRPC_19-050I1_RETROPERITONEAL_LN

source_name: CRPC retroperitoneal lymph node (LN) metastasis


title: mCRPC_20-013_SKIN_MET3


title: mCRPC_20-008L1_RETROP_LN

source_name: CRPC retrop lymph node (LN) metastasis


title: mCRPC_16-052H1_LIVER


title: mCRPC_15-096L2_PERIAORTIC

source_name: CRPC periaortic metastasis


title: mCRPC_16-052K1_LN

source_name: CRPC lymph node (LN) metastasis


title: mCRPC_15-096FF1_BONE

source_name: CRPC bone metastasis


title: mCRPC_15-096M1_PERIAORTIC_DIAPHRAGM

source_name: CRPC periaortic diaphragm metastasis


title: mCRPC_15-090H1_LIVER


title: mCRPC_15-090KK1_BONE


title: mCRPC_15-069P5_LN


title: mCRPC_18-078L3_LIVER


title: mCRPC_15-069M2_PERIOAORTIC_LN

source_name: CRPC perioaortic lymph node (LN) metastasis


title: mCRPC_18-078I2_LUNG

source_name: CRPC lung metastasis


title: mCRPC_15-069K1_LIVER


title: mCRPC_18-082M2_LIVER


title: mCRPC_18-082J2_LN


title: mCRPC_15-023M1_LUNG


title: mCRPC_17-017I1_LIVER


title: mCRPC_15-023L2_LN


title: mCRPC_18-059M4_LN


title: mCRPC_18-059L1_LN


title: mCRPC_18-050K4_BLADDER_WALL

source_name: CRPC bladder wall metastasis


title: mCRPC_18-002J1_LIVER


title: mCRPC_17-113O4_PELVIC_LN


title: mCRPC_15-023K2_SPLEEN

source_name: CRPC spleen metastasis


title: mCRPC_15-010K4_LN


title: mCRPC_17-097K3_LIVER


title: mCRPC_17-072E4_LUNG


title: mCRPC_15-010H1_LIVER


title: 93_Ctrl_EOS_1833_1-5

source_name: LuCaP 93 PDX

value: prostate tumor patient-derived xenograft (PDX)

value: vehicle control

tag: timepoint

value: EOS (end of study)


title: mCRPC_15-003H1_LIVER


title: 93_Ctrl_EOS_1833_1-13


title: 93_CH5183284_EOS_1833_2-13


title: 93_CH5183284_EOS_1833_2-8


title: 49_Ctrl_EOS_2010_1-2

source_name: LuCaP 49 PDX


title: mCRPC_14-105J1_LIVER


title: 49_Ctrl_EOS_2010_1-3


title: mCRPC_18-059H1_LIVER


title: 49_CH5183284_EOS_2010_3-6


title: mCRPC_14-096J1_LEFT_POSTERIOR

source_name: CRPC left posterior metastasis


title: mCRPC_14-091E1_LUNG


title: 147CR_ERDA_EOS_2106_3-4

source_name: LuCaP 147CR PDX

value: erdafitinib (30 mg/kg)


title: 147CR_ENZA_ERDA_EOS_2106_4-4

value: combination enzalutamide (50 mg/kg) + erdafitinib (30 mg/kg)


title: 147CR_ENZA_ERDA_EOS_2106_4-5


title: 147CR_ERDA_EOS_2106_3-3


title: 49_CH5183284_EOS_2010_3-5


title: mCRPC_14-077N15_LIVER


title: mCRPC_14-053O7_LN


title: 147CR_ENZA_EOS_2106_2-3

value: enzalutamide (50 mg/kg)


title: 147CR_Ctrl_EOS_2106_1-5


title: 147CR_Ctrl_EOS_2106_1-3


title: 96CR_ERDA_EOS_2042_3-4

source_name: LuCaP 96CR PDX


title: mCRPC_14-053H3_LIVER


title: 96CR_ERDA_EOS_2042_3-1


title: mCRPC_14-043H6_LIVER


title: 96CR_ENZA_ERDA_EOS_2042_4-3


title: 147CR_ENZA_EOS_2106_2-5


title: 176_ERDA_EOS_2039_3-4

source_name: LuCaP 176 PDX


title: 96CR_Ctrl_EOS_2042_1-4


title: mCRPC_14-039E3_LUNG


title: 96CR_ENZA_ERDA_EOS_2042_4-1


title: mCRPC_14-031L2_PLEURAL

source_name: CRPC pleural metastasis


title: 96CR_Ctrl_EOS_2042_1-1


title: mCRPC_14-043CC3_BONE


title: mCRPC_14-039K4_LIVER

source_name: CRPC liver metastasis


title: mCRPC_14-053K7_LN


title: 176_ENZA_ERDA_EOS_2039_4-3


title: 176_ENZA_EOS_2039_2-1


title: 176_Ctrl_EOS_2039_1-3


title: 96CR_ENZA_EOS_2042_2-3


title: 176_ERDA_EOS_2039_3-3


title: mCRPC_14-031H2_LIVER


title: mCRPC_13-122H1_PELVIC_MASS

source_name: CRPC pelvic mass metastasis


title: 136CR2_ERDA_EOS_2035_3-1

source_name: LuCaP 136CR2 PDX


title: 136CR2_ENZA_ERDA_EOS_2035_4-1


title: mCRPC_13-104I3_LN

source_name: CRPC lymph node (LN) metastasis


title: 96CR_ENZA_EOS_2042_2-1


title: 136CR2_ENZA_EOS_2035_2-3


title: mCRPC_13-104AA2_BONE

source_name: CRPC bone metastasis


title: mCRPC_13-104K7_LN


title: 136CR2_Ctrl_EOS_2035_1-3


title: 176_ENZA_ERDA_EOS_2039_4-4


title: 136CR2_Ctrl_EOS_2035_1-1


title: mCRPC_13-101H1_LN


title: mCRPC_13-084H5_LIVER


title: mCRPC_13-042M3_LN


title: mCRPC_13-117H7_LIVER


title: 176_Ctrl_EOS_2039_1-1


title: mCRPC_13-012M3_LUNG


title: NCI-H660_B

source_name: NCI-H660 (ATCC, CRL-5813) human prostate tumor cell line

growth_protocol: Cells were cultured in their normal growth media.

value: prostate tumor cell line


title: mCRPC_13-012L2_LIVER


title: 136CR2_ERDA_EOS_2035_3-3


title: 22Rv1_B

source_name: 22Rv1 (ATCC, CRL-2505) human prostate tumor cell line


title: mCRPC_13-101K3_LN


title: DU145_B

source_name: DU145 (ATCC, HTB-81) human prostate tumor cell line

value: DU145 (ATCC, HTB-81)


title: DU145_A


title: 136CR2_ENZA_ERDA_EOS_2035_4-3


title: 22Rv1_A


title: VCaP_A

source_name: VCaP (ATCC, CRL-2876) human prostate tumor cell line

value: VCaP (ATCC, CRL-2876)


title: mCRPC_13-042O2_Liver


title: 136CR2_ENZA_EOS_2035_2-5


title: LNCaP_APIPC_B

source_name: LNCaP-APIPC human prostate tumor cell line

value: LNCaP-APIPC


title: LNCaP_APIPC_C


title: LNCaP_C42B_B

source_name: C4-2B (ATCC, CRL-3315) human prostate tumor cell line


title: LNCaP_C42B_A


title: 173.2A_FGFRinh_3-5wk_1618_2-19

source_name: LuCaP 173.2A PDX


title: 173.2A_FGFRinh_3-5wk_1618_2-18


title: 173.2A_Ctrl_3-5wk_1618_1-15


title: 173.2A_Ctrl_3-5wk_1618_1-14


title: 173.1_FGFRinh_3-5wk_1617_2-7

source_name: LuCaP 173.1 PDX


title: 173.1_FGFRinh_3-5wk_1617_2-1


title: 173.1_Ctrl_3-5wk_1617_1-13


title: NCI-H660_A


title: 35CR_FGFRi_1746_10

source_name: LuCaP 35CR PDX


title: 173.1_Ctrl_3-5wk_1617_1-12


title: 35CR_ENZ_FGFRi_1746_6

value: combination enzalutamide (50 mg/kg) + CH5183284 (80 mg/kg)


title: 35CR_ENZ_1746_11


title: VCaP_B


title: 35CR_Ctrl_1746_4


title: 147CR_ENZ_1748_11

source_name: LuCaP 147CR PDX


title: 176_FGFRi_1738_10

source_name: LuCaP 176 PDX


title: 147CR_FGFRi_1748_10


title: 136CR_FGFRi_1747_10

source_name: LuCaP 136CR PDX


title: 136CR_ENZ_FGFRi_1747_6


title: 147CR_Ctrl_1748_4


title: 136CR_ENZ_1747_8


title: 176_Ctrl_1738_3


title: 147CR_ENZ_FGFRi_1748_8


title: 176_ENZ_1738_8


title: 136CR_Ctrl_1747_4


title: Post-transplant, aGVHD, rep2

status: Public on Sep 14 2023

city: CHAPEL HILL

first: SONIA

last: LAURIE

state: NC

address: 125 Mason Farm Road

institute: UNC CHAPEL HILL

description:
Tn5 cut DNA
10x Genomics

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.0.0. Addiitonal analyses were performed using Seruat v.4.3.0.
Assembly: hg38
Supplementary files format and content: h5 (count matrix), ATAC fragment file, fragment index file, bed file (cellRanger_atac_peakcalls), csv file (cellRanger_per_barcode_info).

source_name: PBMC

extract_protocol:
Cells were removed from liquid nitrogen and thawed in aMEM supplemented with 10% FBS and a DNASe-containing dextran-Albumin solution. We utilized a bead based magnetic separation approach to isolate live cells.
Viable cells were counted and then scATAC libraries were prepared using the 10x Chromium Chromium Next GEM Single Cell ATAC Kit v2 (cat # 1000406). These ATAC libraries were technically single index, but were sequenced in a dual index format (50x8x16x50) and were sequenced at a depth of 25-50,000 read pairs per cell on either the Illumina NextSeq2000P2 or Illumina NovaSeq SP.

value: PBMC

tag: group

value: Post-transplant, aGVHD


title: Post-transplant, aGVHD, rep3

description:
Tn5 cut DNA
10x Genomics


title: Post-transplant, no_aGVHD_rep3

description:
Tn5 cut DNA
10x Genomics

value: Post-transplant, no_aGVHD_rep3


title: Post-transplant, aGVHD, rep1

description:
Tn5 cut DNA
10x Genomics


title: Post-transplant, no_aGVHD_rep1

description:
Tn5 cut DNA
10x Genomics

value: Post-transplant, no_aGVHD_rep1


title: Post-transplant, no_aGVHD_rep2

description:
Tn5 cut DNA
10x Genomics

value: Post-transplant, no_aGVHD_rep2


title: Pre-transplant, future_aGVHD, rep3

description:
Tn5 cut DNA
10x Genomics

value: Pre-transplant, future_aGVHD


title: 176_ENZ_FGFRi_1738_1

value: male

value: prostate tumor patient-derived xenograft (PDX)

value: prostate cancer


title: Pre-transplant, no_future_aGVHD, rep1

description:
Tn5 cut DNA
10x Genomics

value: Pre-transplant, no_future_aGVHD


title: Healthy Donor, rep2

description:
Tn5 cut DNA
10x Genomics

value: Healthy Donor


title: Healthy Donor, rep1

description:
Tn5 cut DNA
10x Genomics


title: GFP+ ILC2, cytokine treated, rep2, snATAC-Seq

description:
Tn5 cut DNA
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.0.0. Addiitonal analyses were performed using Seruat v.4.3.0.
Assembly: mm10
Supplementary files format and content: h5 (count matrix), ATAC fragment file, fragment index file, bed/csv files (cellRanger_atac_peakcalls).

source_name: mesenteric lymph nodes and peritoneum

extract_protocol:
(in vitro) ILC2 + pcILC2: Lineage negative, ST2+ cells from the peritoneum and mesenteric lymph nodes were isolated and expanded in culture for 2 days in the presence of recombinant IL-7 and IL-33. ILC2s were expanded in IL-7 and IL-33 for 4 additional days, while the pcILC2 cells were treated with IL-12, IL-1b, and IL-18 (pcILC2). (ex vivo) GFP+ exILC2 post-BMT: Animals were euthanized with CO2 and the small intestine lamina propria (LP) was excised. LP lymphocytes were isolated using the Miltenyi LP dissociation kit (catalog 130-097-410) as per the manufacturer’s instructions. Livers and lungs were digested in a solution of 1 mg/ml collagenase A (Roche) and 75 U DNase I (Sigma-Aldrich) in RPMI 1640 with 5% newborn calf serum. Digested tissues were treated with ACK lysis buffer to remove RBCs and were passed through 100 μm cell strainers. Leukocytes were collected at the interface of a 40%:80% Percoll (Sigma-Aldrich) gradient in RPMI 1640 with 5% NCS. The pelleted cells were washed in 1x DPBS with 2% FBS. Spleens and MLN were teased apart, treated with ACK lysis buffer, and washed in 1 x DPBS with 2% FBS.
For all experiments, library preparation was performed according to the manufacturer’s instructions (see Single Cell Chromium Next GEM Multiome ATAC+GEX, 10x Genomics, CG000338, Rev D). Nuclei were isolated from sorted GFP+ cells following the ‘Low Cell Input Nuclei Isolation’ protocol (CG000365, Rev C) where lysis buffer was used at 1x and lysis proceeded for 4 minutes.
10X Multiome

value: mesenteric lymph nodes and peritoneum

tag: age

value: 8-20 weeks old


title: GFP+ ILC2, cytokine treated, rep2, snRNA-Seq

description:
nuclear RNA
10x Genomics

library_source: transcriptomic single cell

molecule: nuclear RNA


title: GFP+ ILC2, cytokine treated, rep1, snRNA-Seq

description:
nuclear RNA
10x Genomics


title: GFP+ ILC2, cytokine treated, rep1, snATAC-Seq

description:
Tn5 cut DNA
10x Genomics


title: GFP+ ILC2, pre-transplant, rep2, snATAC-Seq

description:
Tn5 cut DNA
10x Genomics


title: GFP+ ILC2, pre-transplant, rep2, snRNA-Seq

description:
nuclear RNA
10x Genomics


title: GFP+ ILC2, pre-transplant, rep1, snATAC-Seq

description:
Tn5 cut DNA
10x Genomics


title: ILC2, H3K4me3, rep2

data_processing:
Basecalls were performed using bcl2fastq
cutadapt (v. 1.12) was used to trim addaptor sequences. Reads were quality filtered using FASTX-ToolKit (v0.0.12) with paramters Q 33, -p 90, and q 20. Reads were aligned to mm10 mouse genome using STAR (v2.5.2b).
Peaks were called uing MACS v2.1.2 usingdefault parameters
Assembly: mm10
Supplementary files format and content: bigWig files contain total read depth normalized signal, narrowPeak files contain MACS2 peak calls.

extract_protocol:
Lineage negative, ST2+ cells from the peritoneum and mesenteric lymph nodes were isolated and expanded in culture for 6 days in the presence of recombinant IL-7 and IL-33 as previously described (Bruce et al, J Clin Invest, 2017 and Bruce et al, Blood Advances, 2022).
2.5 - 5x106 cells were pelleted prior to fixation with and fixed with a 1% formaldehyde using the ChIP-IT High Sensitivity Kit (Active Motif). After quenching and washing, pellets were frozen at −80°C. Upon thawing, cells were sheared using a chilled dounce homogenizer using with the ChIP-IT High Sensitivity Kit (Active Motif) and lysed cells were sonicated with nanodroplets for 60 seconds with the Covaris Le220 prior to clarified by centrifuging at full speed for 15 min. Input DNA was prepared with RNase A and Proteinase K prior to clean up and concentration with the Zymo Chip DNA Clean and Concentrate kit. 10-30 ug of ILC chromatin were treated with an anti-H3K4me3 antibody (Cell Signaling Technologies, rabbit mAb 9751, clone C42D8) + blocker mix along with a protease inhibitor cocktail prior to overnight end-to-end rotation at 4°C. 30 μL of Protein G Dynabeads were added to each 240 μL immunoprecipitation reaction, and reactions were incubated for 3 h. Samples were passed through a ChIP Filtration Column and then washed 5x with Wash Buffer AM1. After removal of residual wash buffer, samples were eluted in pre-warmed elution buffer AM4. De-crosslinking was carried out for 2.5h with Proteinase K prior to DNA extraction with the ChIP DNA Clean & Concentrator (Zymo Research) protocol. Chromatin immunoprecipitation quantitative real-time PCR (ChIP-qPCR) was performed using the QuantStudio 6K from Applied Biosystems.

tag: chip antibody

value: Cell Signaling Technologies, anti-H3K4 rabbit mAb, cat # 9751, clone C42D8


title: ILC2, H3K4me3, rep1


title: GFP+ ILC2, pre-transplant, rep1, snRNA-Seq

description:
nuclear RNA
10x Genomics

tag: tissue


title: Pre-transplant, no_future_aGVHD, rep2

description:
Tn5 cut DNA
10x Genomics


title: Pre-transplant, future_aGVHD, rep2

description:
Tn5 cut DNA
10x Genomics


title: pcILC2, ATAC, rep2

description: 1x75 high output

data_processing:
Basecalls were performed using bcl2fastq
cutadapt (v. 1.12) was used to trim addaptor sequences. Reads were quality filtered using FASTX-ToolKit (v0.0.12) with paramters Q 33, -p 90, and q 20. Reads were aligned to mm10  mouse genome or hg38 human genome using STAR (v2.5.2b).
Peaks were called uing MACS v2.1.2 usingdefault parameters
Assembly: mm10 and hg38
Supplementary files format and content: bigWig files contain total read depth normalized signal, narrowPeak files contain MACS2 peak calls / DESeq2_peaks.

source_name: murine pcILC2

extract_protocol:
Human ILC2s were isolated from a TrimaAccel LRS Chamber containing peripheral blood of health donors with the RosetteSep Human ILC2 Enrichment Kit (Stem Cell). ILC2s and pro-inflammatory conditioned ILC2s (pcILC2s) were cultured at 2.25 x 105 cells/mL in aMEM medium supplemented with 20% FBS and 1% Pen-Strep along with 50 ng/ml rIL-7, IL-2, IL-25, IL-4 and rIL-33 for the ILC2s and 50 ng/ml rIL-7, 50 ng/ml rIL-12, IL-2, rIL-1b, and 25 ng/ml rIL-18. After 14-21 days, viability and purity was assessed by flow cytometry and nuclei were isolated by pelleting 25,000 - 200,000 in a fixed-angle centrifuge. Mouse ILC2s were cultured at 2.25 x 10^5 cells/mL for 6 days in complete media (RPMI-1640 supplemented with 10% FBS, 2 mM L-glutamine, 12 mM HEPES, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 1% Pen/Strep, and 50 μM 2-mercaptoethanol) and supplemented with 10 ng/ml rIL-7 and rIL-33 (PeproTech), with the media changed every 2 days. For experiments in which cells were generated via cytokine-mediated skewing (pcILC2s), cells were cultured at 2.25 x 105 cells/mL for 48 hours in complete media supplemented with 10 ng/ml rIL-7 and rIL-33 (PeproTech). On Days 2 and 4, the media was replaced with complete R10 containing 10 ng/ml rIL-7, 10 ng/ml rIL-12, 10 ng/ml rIL-1b, 10 ng/ml rIL-15, 10 ng/ml rIL-2, and 5 ng/ml rIL-18.
For library preparation for both mouse and human ILC2s, cells were lysed prior to 30 minutes of transposition with an in house Tn5 transposase at 37°C. Immediately following transposition, samples were purified with Zymo Conc & Clean (Genesee) and stored at -20°C prior to library amplification. Fragments were amplified using 1× NEBnext PCR master mix (New England BioSciences) and custom Nextera PCR primers. Full libraries were amplified for five cycles, after which a test aliquot of each sample was taken to test 20 cycles to determine the additional number of cycles needed for the remaining 45 μL reaction. After the additional cycles were complete (average of 5-15 additional cycles), libraries were purified prior to a two-sided Ampure bead (Beckman Coulter) size selection to enrich for nucleosome-free fragments. Fragment size and concentration were determined by TapeStation 2000 and Qubit 4 (Agilent).

value: murine pcILC2


title: pcILC2, ATAC, rep1

description: 1x75 high output


title: Pre-transplant, no_future_aGVHD, rep3

description:
Tn5 cut DNA
10x Genomics


title: ILC2, ATAC, rep3

description: 1x75 high output

source_name: murine ILC2

value: murine ILC2


title: Pre-transplant, future_aGVHD, rep1

description:
Tn5 cut DNA
10x Genomics


title: pc-hILC2, ATAC, rep2

description: read length 2x50

source_name: human pcILC2

value: human pcILC2


title: ILC2, ATAC, rep2

description: 1x75 high output


title: pc-hILC2, ATAC, rep1

description: read length 2x50


title: hILC2, ATAC, rep2

description: read length 2x50

source_name: human ILC2

value: human ILC2


title: ILC2, ATAC, rep1

description: 1x75 high output


title: hILC2, ATAC, rep1

description: read length 2x50


title: Isolated ILC2, Healthy Donor, rep1

description:
Tn5 cut DNA
10x Genomics

value: PBMC

value: Isolated ILC2, Healthy Donor


title: GFP+ ILC2, post-transplant, rep1, snRNA-Seq

description:
nuclear RNA
10x Genomics

source_name: lamina propria

value: lamina propria

value: 8-16 weeks old


title: GFP+ ILC2, post-transplant, rep2, snATAC-Seq

description:
Tn5 cut DNA
10x Genomics


title: GFP+ ILC2, post-transplant, rep2, snRNA-Seq

description:
nuclear RNA
10x Genomics


title: T21 CA IFN rep3

status: Public on Sep 12 2023

city: Boulder

first: Meaghan

last: Courvan

state: CO

address: 596 UCB

department: Biofrontiers

institute: University of Colorado, Boulder

description: RNA-seq from Trisomy 21 lymphoblastoid cells

data_processing:
Read trimming using bbduk (options: ktrim=r qtrim=r1, trimq=10, k=23 mink=11 hdist=1 maq=10 minlen=25 tpe tbo literal=AAAAAAAAAAAAAAAAAAAAAAA)
Reads were mapped to hg38 using hisat2
Reads over hg38 refseq gene annotations were counted using featurecounts and then RPKM normalized. Highest average RPKM isoform (across replicates and treatments) was retained in cases where multiple isoform annotations existed
Normalization of samples based on size factors and statistical analysis of comparisons between experimental condtions were performed using DESEQ2; for intergenotype (T21 vs D21) comparisons, expression of genes on chromosome 21 was normalized to account for ploidy
Tdfs were generated from trimmed BAM files using igvtools
Splicing analysis was performed with rMATS (4.0.1) and sashimi plots were generated from rMATs result using a modified script based on ggsashimi.py
Assembly: hg38
Supplementary files format and content: csv file with log2fold change and adj p-value for each gene for each comparison, both within-genotype (looking at treatmetn effects) and between-genotype (looking at basal differences in T21 vs D21 or differential effects of treatment)

source_name: Trisomy 21 immortalized lymphoblastoid

growth_protocol: Lymphoblastoid suspension cells were grown in RPMI medium supplemented with 20% fetal bovine serum, pennicilin/strep, and L-glutamine

extract_protocol:
4 hours after vehicle or IFNγ treatment, cells were collected, spun down, washed once in PBS, then resuspended in TRIzol reagent (Invitrogen, 15596026) and snap frozen. After all 3 biological replicates were collected, cell lysates in TRIzol were thawed and total RNA was extracted according to the manufacturer's protocol. RNA concentration was measured by Qubit and quality was verified using a TapeStation
Protocol for Universal Plus™ mRNA-Seq library preparation kit with NuQuant® (Tecan, 0520) was used
Universal Plus™ mRNA-Seq library preparation kit with NuQuant® (Tecan, 0520)

treatment_protocol: Cells were split and plated on T75 flasks, allowed to recover for 24 hours, then media containing either vehicle (final concentration 0.01% DMSO) or Cortistatin A (100 nM) was added to each flask. After 30 minutes, media containing either vehicle (final concentration 40 μM Tris pH 7.4) or 10 ng/mL recombinant IFNγ (Gibco, PHC4031)

value: Trisomy 21 immortalized lymphoblastoid

value: immortalized lymphoblastoid

value: 100 nM Cortistatin A + 10 ng/mL IFNγ

tag: treatment delivery method

value: Treatment diluted in media and added to flasks with cells

tag: molecule type

value: Small molecule + cytokine


title: T21 CA IFN rep2


title: GFP+ ILC2, post-transplant, rep1, snATAC-Seq

description:
Tn5 cut DNA
10x Genomics


title: T21 CA V rep2

value: 100 nM Cortistatin A + 40 μM Tris pH 7.4


title: T21 V IFN rep3

value: 0.01% DMSO + 10 ng/mL IFNγ


title: T21 CA V rep1


title: T21 CA V rep3


title: T21 CA IFN rep1


title: T21 V IFN rep2


title: T21 V IFN rep1


title: T21 V V rep2

value: 0.01% DMSO + 40 μM Tris pH 7.4


title: D21 CA V rep3

description: RNA-seq from euploid lymphoblastoid cells

source_name: Euploid immortalized lymphoblastoid

value: Euploid immortalized lymphoblastoid


title: T21 V V rep1


title: D21 CA V rep2


title: D21 V IFN rep2


title: D21 CA IFN rep2


title: D21 CA IFN rep3


title: D21 V IFN rep1


title: D21 CA V rep1


title: D21 CA IFN rep1


title: D21 V V rep2


title: D21 V V rep3


title: D21 V V rep1


title: ffff248

city: Baltimore

first: Michael

middle: J.

last: Wolfgang

state: MD

address: 855 N Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: The Johns Hopkins University School of Medicine

description:
gene_count.txt
gene_fpkm.txt
TotalNormCounts041123v2.txt
Rab30_AlbCrevsRab30Cpt2_f_deg.txt
R30C2_AlbCrevsCpt2_AlbCre_deg.txt
Cpt2_AlbCrevsRab30Cpt2_f_deg.txt

data_processing:
Raw reads were filtered to remove reads containing adapters or reads of low quality.
Clean reads were mapped to the reference genome (GRCm38/mm10) using the HISAT2 software.
Gene counts were extracted and gene expression levels were estimated by the expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM).
Pairwise comparisons of differential gene expression analysis was performed by read count normalization, model dependent p-value estimation, and FDR value estimation based on multiple hypothesis testing by Novogene's standard procedures.
Downstream analysis using the DESeq2 package in R was performed independently by the investigators to normalize raw read counts for comparisons across all samples.
Assembly: GRCm38/mm10
Supplementary files format and content: gene_count.txt includes raw readcount list with the annotation of each gene for each sample. Tab-delimited text file.
Supplementary files format and content: gene_fpkm.txt includes the FPKM list with the annotation of each gene for each sample.Tab-delimited text file.
Supplementary files format and content: TotalNormCounts041123v2.txt includes the downstream DESeq2 analysis (with Wald test, betaPrior=FALSE, and genes with at least 1 count) performed by the investigators with normalized read counts and the annotation of each gene for each sample.Tab-delimited text file.
Supplementary files format and content: Rab30_AlbCrevsRab30Cpt2_f_deg.txt includes the differential analysis results of all genes when comparing Rab30 liver-specific KO samples to Rab30;Cpt2 floxed control (littermates to DKO) samples. Tab-delimited text file.
Supplementary files format and content: Rab30KOvsRab30WT_deg.txt includes the differential analysis results of all genes when comparing Rab30 whole-body KO to WT littermates to Rab30 whole-body KO. Tab-delimited text file.
Supplementary files format and content: R30C2_AlbCrevsCpt2_AlbCre_deg.txt includes the differential analysis results of all genes when comparing Rab30;Cpt2 liver-specific DKO to Cpt2 liver-specific KO. Tab-delimited text file.
Supplementary files format and content: Cpt2_AlbCrevsRab30Cpt2_f_deg.txt includes the differential analysis results of all genes when comparing Cpt2 liver-specific KO to Rab30;Cpt2 floxed control (littermates to DKO). Tab-delimited text file.
Supplementary files format and content: R30C2_AlbCrevsRab30Cpt2_f_deg.txt includes the differential analysis of all genes when comparing Rab30;Cpt2 liver-specific DKO to Rab30;Cpt2 flozed control (littermates to DKO). Tab-delimited text file.

source_name: liver

extract_protocol:
Total RNA was extracted from flash frozen liver tissue using TRIzol reagent (Invitrogen for Thermo Fisher Scientific, 15596026) with additional purification using RNeasy Mini Kit (Qiagen, 74106), as per manufacturers’ instructions. RNA quality was assessed by nanodrop and independently by Novogene Corporation Inc (https://en.novogene.com/services/research-services/transcriptome-sequencing/).
RNA libraries for RNA-seq were prepared by Novogene following Novogene's standard protocols.

value: liver

value: 24hr fast


title: Cpt2801

description:
gene_count.txt
gene_fpkm.txt
TotalNormCounts041123v2.txt
R30C2_AlbCrevsCpt2_AlbCre_deg.txt
Cpt2_AlbCrevsRab30Cpt2_f_deg.txt

value: Cpt2 liver-specific KO


title: T21 V V rep3


title: ffff242

value: Rab30;Cpt2 floxed control (littermates to DKO)


title: ffff238


title: ffff240